Require R4.1

.github/workflows/R-CMD-check.yml

@@ -47,8 +47,8 @@ jobs:
         config:
           - {os: windows-latest, r: 'release'}
           - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: '4.0', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: '4.1', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"} # Until TreeDist can slough phangorn
-          #- {os: ubuntu-20.04, r: '3.6', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
@@ -79,7 +79,7 @@ jobs:
         if: runner.os == 'macOS'
         run: |
           brew install libgit2 xquartz ghostscript
-      
+
       - name: Set up R dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:

.github/workflows/gcc-ASAN.yml

@@ -66,7 +66,7 @@ jobs:
 
       - name: Setup pandoc
         if: ${{ matrix.config.test }} == 'vignettes'
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |

.github/workflows/update-csl.yml

@@ -0,0 +1,31 @@
+name: Update CSL file
+on:
+  schedule:
+    - cron: '0 0 * * 1'  # Runs weekly on Monday at 00:00 UTC
+  workflow_dispatch:      # Allows manual triggering
+
+jobs:
+  update-csl:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download latest CSL file
+        run: |
+          curl -o inst/apa-old-doi-prefix.csl https://raw.githubusercontent.com/citation-style-language/styles/master/apa-old-doi-prefix.csl
+
+      - name: Check for changes
+        id: changes
+        run: |
+          if git diff --quiet; then
+            echo "No changes to commit"
+            exit 0
+          fi
+
+      - name: Commit and push if changed
+        run: |
+          git config --local user.email "actions@github.com"
+          git config --local user.name "GitHub Actions"
+          git add inst/apa-old-doi-prefix.csl
+          git commit -m "Update CSL file from upstream"
+          git push

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: TreeSearch
 Title: Phylogenetic Analysis with Discrete Character Data
-Version: 1.5.1.9003
+Version: 1.5.1.9005
 Authors@R: c(
     person(
       "Martin R.", 'Smith',
@@ -32,7 +32,7 @@ Description: Reconstruct phylogenetic trees from discrete data.
 URL: https://ms609.github.io/TreeSearch/ (doc),
   https://github.com/ms609/TreeSearch/ (devel)
 BugReports: https://github.com/ms609/TreeSearch/issues/
-Depends: R (>= 3.5.0)
+Depends: R (>= 4.0)
 Imports: 
   ape (>= 5.6),
   cli (>= 3.0),

NEWS.md

@@ -1,3 +1,8 @@
+# TreeSearch 1.5.1.9005 (2025-02)
+
+- Support for ordered (additive) characters
+- Require R 4.0 (to simplify maintenance)
+
 # TreeSearch 1.5.1.9003 (2025-02)
 
 - Improve support for constraints in `AdditionTree()`
@@ -7,12 +12,14 @@
 
 - Buttons to download consensus trees in app
 
-
 # TreeSearch 1.5.1.9001 (2024-12)
 
-- Fix display of state labels in app
 - Fix SPR behaviour when move is close to root
 
+# TreeSearch 1.5.1.9000 (2024-10)
+
+- Fix display of state labels in app
+
 
 # TreeSearch 1.5.1 (2024-05-23)
 

R/AdditionTree.R

@@ -53,6 +53,7 @@ AdditionTree <- function (dataset, concavity = Inf, constraint, sequence) {
   attr(dataset, "info.amounts") <- NULL
   attr(dataset, "min.length") <- NULL
   attr(dataset, "informative") <- NULL
+  attr(dataset, "originalIndex") <- NULL
 
   # Starting tree, rooted on first element in sequence
   tree <- PectinateTree(sequence[1:3])

R/NNI.R

@@ -93,8 +93,12 @@ NNI <- function (tree, edgeToBreak = NULL) {
 #' @export
 cNNI <- function (tree, edgeToBreak = NULL, whichSwitch = NULL) {
   edge <- tree[["edge"]]
-  if (is.null(edgeToBreak)) edgeToBreak <- sample.int(dim(edge)[1] - NTip(tree) - 1L, 1L)
-  if (is.null(whichSwitch)) whichSwitch <- sample.int(2L, 1L)
+  if (is.null(edgeToBreak)) {
+    edgeToBreak <- sample.int(dim(edge)[[1]] - NTip(tree) - 1L, 1L)
+  }
+  if (is.null(whichSwitch)) {
+    whichSwitch <- sample.int(2L, 1L)
+  }
   tree[["edge"]] <- nni(edge, edgeToBreak, whichSwitch)
 
   # Return:

README.md

@@ -106,7 +106,7 @@ Brazeau, M. D., Guillerme, T. and Smith, M. R. (2019).
 Faith D. P., Trueman J. W. H. (2001).
   Towards an inclusive philosophy for phylogenetic inference.
   Systematic Biology, 50(3), 331–350. 
-  doi: [10.1080/10635150118627](https://doi.org/10.1080/10635150118627).
+  doi: [10.1080/10635150118627](https://dx.doi.org/10.1080/10635150118627).
 
 Farris, J. S. (1969). A successive approximations approach to character weighting. 
   Systematic Biology, 18(4), 374–385.

codemeta.json

@@ -8,13 +8,13 @@
   "codeRepository": "https://github.com/ms609/TreeSearch/",
   "issueTracker": "https://github.com/ms609/TreeSearch/issues/",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "1.5.1.9002",
+  "version": "1.5.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 4.4.2 (2024-10-31)",
+  "runtimePlatform": "R version 4.4.0 (2024-04-24)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -380,7 +380,7 @@
     },
     "SystemRequirements": "C++17"
   },
-  "fileSize": "4469.809KB",
+  "fileSize": "4467.376KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -452,7 +452,7 @@
       ],
       "name": "{TreeSearch}: phylogenetic analysis with discrete character data",
       "identifier": "10.5281/zenodo.1042590",
-      "description": "R package version 1.5.1.9002",
+      "description": "R package version 1.5.1",
       "@id": "https://doi.org/10.5281/zenodo.1042590",
       "sameAs": "https://doi.org/10.5281/zenodo.1042590"
     },

man-roxygen/datasetParam.r

@@ -1,3 +1,4 @@
 #' @param dataset A phylogenetic data matrix of \pkg{phangorn} class
 #' \code{phyDat}, whose names correspond to the labels of any accompanying tree.
+#' Perhaps load into R using \code{\link[TreeTools]{ReadCharacters}}.
 # Defined in TreeTools.  Please propagate any changes there.

tests/testthat/test-CustomSearch.R

@@ -10,7 +10,7 @@ RootySwappers <- list(RootedTBRSwap, RootedSPRSwap, RootedNNISwap)
 test_that("Tree can be found", {
   skip_if_not_installed("phangorn")
   phy11 <- phangorn::phyDat(data11, type = "USER", levels = c(FALSE, TRUE))
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
+  RNGkind("Mersenne-Twister")
   set.seed(1)
   random11 <- as.phylo(17905853L, 11, letters[1:11])
   expect_error(TreeSearch(unrooted11, dataset = phy11))
@@ -110,7 +110,7 @@ test_that("Profile parsimony works in tree search", {
   dataset <- TreeTools::PhyDat(sillyData)
   readyData <- PrepareDataProfile(dataset)
 
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
+  RNGkind("Mersenne-Twister")
   set.seed(0)
 
   rTree <- randomTree <- RandomTree(dataset, "1")

tests/testthat/test-Jackknife.R

@@ -11,7 +11,7 @@ test_that("Jackknife supports are correct", {
   expect_error(Jackknife(start_tree, dataset, resampleFreq = 0))
   expect_error(Jackknife(start_tree, dataset, resampleFreq = 9/10))
 
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
+  suppressWarnings(RNGversion("3.5.0"))
   set.seed(0)
 
   strict <- TreeSearch(start_tree, dataset, verbosity = 0)

tests/testthat/test-pp-random-tree.R

@@ -38,7 +38,6 @@ test_that("four-tip trees are randomly distributed", {
 })
 
 test_that("four-tip trees are randomly scored", {
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
   set.seed(0)
 
   nTrees <- 6000
@@ -57,7 +56,6 @@ test_that("four-tip trees are randomly scored", {
 })
 
 test_that("five-tip trees are randomly scored", {
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
   set.seed(0)
   nTrees <- 6000
   stringency <- 0.005
@@ -75,7 +73,6 @@ test_that("five-tip trees are randomly scored", {
 
 
 test_that("six-tip trees are randomly scored", {
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
   set.seed(0)
 
   nTrees <- 6000

tests/testthat/test-zzz-tree-rearrange.R

@@ -46,7 +46,7 @@ test_that("NNI works", {
   Test(2, 0, 3, 9)
   Test(2, 1, 8, 9)
 
-  suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
+  suppressWarnings(RNGversion("3.5.0"))
   set.seed(0)
   nniComb <- NNI(trComb)
   expect_equal(nniComb$tip.label, trComb$tip.label)
@@ -57,7 +57,7 @@ test_that("NNI works", {
 
 test_that("SPR works", {
   testTree <- Preorder(root(BalancedTree(7), 1, resolve.root = TRUE))
-  edge <- testTree$edge
+  edge <- testTree[["edge"]]
   expect_equal(spr(edge, 66), cSPR(testTree, 66)$edge)
 
   Test <- function (m, p1, r1) {
@@ -243,7 +243,7 @@ CheckTreeSanity <- function (tree) {
                info=paste0("Root is numbered ", min(parent), "; expecting ", nTip + 1)
   )
   expect_false(min(parent) %in% child, 
-               info=paste0("Root node (", min(parent), ") is child of edge ", paste0(which(min(parent) == child), collapse=', '))
+               info=paste0("Root node (", min(parent), ") is child of edge ", paste0(which(min(parent) == child), collapse = ", "))
   )
   expect_true(all(seq_len(nTip) %in% child)) # No missing tips
   expect_equal(max(parent), nTip + nNode)
@@ -252,7 +252,7 @@ CheckTreeSanity <- function (tree) {
   expect_true(all(child[!tips] > parent[!tips]), info="Parent nodes must be > child nodes")
 }
 
-suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
+suppressWarnings(RNGversion("3.5.0"))
 set.seed(0)
 small_tree <- rtree(8)
 large_tree <- rtree(80)  

vignettes/getting-started.Rmd

@@ -18,7 +18,7 @@ datasets.
 ### Simple installation
 
 To use "TreeSearch" you will first need to [install R](
-https://CRAN.R-project.org/). 
+https://CRAN.R-project.org/).
 [RStudio](https://posit.co/) is a popular front-end that makes several of R's
 features easier to use.
 

vignettes/profile.Rmd

@@ -40,9 +40,9 @@ library("TreeSearch")
 
 In order to reproduce the random elements of this document, set a random seed:
 
-```{R rng-version}
+```{R rng-version, warn = FALSE}
 # Set a random seed so that random functions in this document are reproducible
-suppressWarnings(RNGversion("3.5.0")) # Until we can require R3.6.0
+RNGversion("3.5.0")
 set.seed(888)
 ```
 

vignettes/tree-search.Rmd

@@ -73,9 +73,9 @@ escape from local optima.
 vinther <- TreeSearch::inapplicable.phyData[["Vinther2008"]]
 ```
 
-```{R RNG-version}
+```{R RNG-version, warn = FALSE}
 # Set a random seed so that random functions in this document are reproducible
-suppressWarnings(RNGversion("3.5.0")) # Until we require R v3.6.0
+RNGversion("3.5.0")
 set.seed(0)
 ```